During the past 15 years, we have carried out several different systematic screens for small regulatory RNA genes in E. coli. These screens have included computational searches for conservation of intergenic regions and direct detection after size selection or co-immunoprecipitation with the RNA binding protein Hfq. We recently examined small RNA expression using deep sequencing to further extend our identification of small RNAs, particularly antisense RNAs (1). A large focus of the group has been to elucidate the functions of the small RNAs we and others have identified. Early on we showed that the OxyS RNA, whose expression is induced in response to oxidative stress, acts to repress translation through limited base pairing with target mRNAs. We discovered OxyS action is dependent on the Sm-like Hfq protein, which functions as a chaperone to facilitate OxyS RNA base pairing with its target mRNAs (2). Recently we carried out an extensive mutational studies of Hfq (3). This analysis revealed that amino acids on three different RNA interaction surfaces--the proximal face, the distal face and the rim of the doughnut-shaped protein--differentially impact Hfq association with small RNAs and their mRNA targets. It is now clear that Hfq-binding small RNAs, which act through limited base pairing, are integral to many different stress responses in E. coli. For example, we showed that the Spot 42 RNA, whose levels are highest when glucose is present, plays a broad role in catabolite repression by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse nonpreferred carbon sources. It was previously reported that the transcription factor Sigma(E) maintains membrane homeostasis in part by inducing synthesis of two small regulatory RNAs that down-regulate synthesis of abundant membrane porins. We discovered of a third Sigma(E)-dependent small RNA, MicL, transcribed from a promoter located within the coding sequence of the cutC gene (4). MicL possesses features typical of Hfq-binding small RNAs but surprisingly targets only a single mRNA, which encodes the outer membrane lipoprotein Lpp, the most abundant protein of the cell. Interestingly, we found that the copper sensitivity phenotype previously ascribed to inactivation of the cutC gene is actually derived from the loss of MicL and elevated Lpp levels. This observation raises the possibility that other phenotypes currently attributed to protein defects are due to deficiencies in unappreciated regulatory RNAs and prompted us to ask questions about the evolution of base pairing small RNAs (5). In addition to small RNAs that act via limited base pairing, we have been interested regulatory RNAs that act by other mechanisms. For example, early work showed that the 6S RNA binds to and modulates RNA polymerase by mimicking the structure of an open promoter. In a more recent study, we discovered that a broadly conserved RNA structure motif, the yybP-ykoY motif, found in the 5-UTR of the mntP gene encoding a manganese exporter directly binds manganese, resulting in a conformation that liberates the ribosome-binding site (6). Remarkably, we were able to recapitulate the effect of manganese-dependent activation of translation in vitro. We also found that the yybP-ykoY motif responds directly to manganese ions in Bacillus subtilis. The identification of the yybP-ykoY motif as a manganese ion sensor suggests the genes that are preceded by this motif, and encode a diverse set of poorly characterized membrane proteins, have roles in metal homeostasis. Studies to further characterize other Hfq-binding RNAs, antisense RNAs and small RNAs that act in ways other than base pairing are ongoing.